Table 2.
Aggregate analysis of (OT-10, OT-11, OT-18, OT-19, OT-23 and OT-24) and control (OC-2, OC-6, OC-22) samples along with other OSCC and control samples processed on Oncoscan array, we identified significant copy number gain and copy number loss showing CNV overlap and frequency
| Region | Region Length | Cytoband Location | Event | Genes | miRNAs | Frequency % | p-value | % of CNV Overlap | Count of Gene Symbols | Cancer Gene Census-Sanger.txt |
|---|---|---|---|---|---|---|---|---|---|---|
| chr2:89,138,631-89,389,171 | 250540 | p11.2 | CN Gain | 0 | 0 | 36.36364 | 0.002 | 100 | 0 | |
| chr3:52,631,633-52,741,160 | 109527 | p21.1 | CN Loss | 9 | 0 | 54.54545 | 0.048 | 0.318643 | 9 | PBRM1 |
| chr3:60,380,259-60,571,437 | 191178 | p14.2 | CN Loss | 1 | 0 | 54.54545 | 0.048 | 25.46527 | 1 | FHIT |
| chr7:55,114,950-55,124,319 | 9369 | p11.2 | CN Gain | 1 | 0 | 81.81818 | 0.004 | 100 | 1 | EGFR |
| chr9:21,903,166-22,027,402 | 124236 | p21.3 | CN Loss | 4 | 0 | 36.36364 | 0.002 | 100 | 4 | |
| chr9:22,028,315-22,140,224 | 111909 | p21.3 | CN Loss | 1 | 0 | 36.36364 | 0.002 | 100 | 1 | |
| chr11:69,508,372-70,096,585 | 588213 | q13.3 | CN Gain | 7 | 0 | 72.72727 | 0.002 | 7.257745 | 7 | |
| chr11:70,120,785-70,158,876 | 38091 | q13.3 | CN Gain | 2 | 1 | 72.72727 | 0.002 | 11.77969 | 2 | |
| chr11:70,172,204-70,289,645 | 117441 | q13.3 | CN Gain | 2 | 0 | 72.72727 | 0.002 | 39.32443 | 2 | |
| chr11:70,295,897-70,420,282 | 124385 | q13.3–q13.4 | CN Gain | 1 | 0 | 72.72727 | 0.002 | 0 | 1 | |
| chr12:132,982,204-133,331,537 | 349333 | q24.33 | CN Loss | 8 | 0 | 36.36364 | 0.001 | 32.73724 | 8 | |
| chr16:1,154,125-1,486,352 | 332227 | p13.3 | CN Loss | 12 | 0 | 45.45455 | 0.01 | 100 | 12 | |
| chr16:1,790,665-2,305,328 | 514663 | p13.3 | CN Loss | 50 | 1 | 45.45455 | 0.01 | 79.73334 | 50 | TSC2 |
| chr16:88,846,849-88,874,778 | 27929 | q24.3 | CN Loss | 2 | 0 | 36.36364 | 0 | 30.77804 | 2 | |
| chr19:1,225,825-1,259,625 | 33800 | p13.3 | CN Loss | 4 | 0 | 45.45455 | 0.038 | 100 | 4 | STK11 |
| chr21:46,869,264-47,061,267 | 192003 | q22.3 | CN Loss | 4 | 0 | 63.63636 | 0.003 | 91.45586 | 4 | |
| chr21:47,155,316-47,841,692 | 686376 | q22.3 | CN Loss | 15 | 0 | 63.63636 | 0.003 | 13.00585 | 15 | |
| chr22:22,266,808-22,289,397 | 22589 | q11.22 | CN Gain | 1 | 0 | 36.36364 | 0.013 | 100 | 1 | |
| chrX:177,942-2,686,899 | 2508957 | p22.33 | CN Gain | 24 | 0 | 63.63636 | 0 | 29.06012 | 24 | CRLF2, P2RY8 |
| chrX:154,479,421-154,929,412 | 449991 | q28 | CN Gain | 26 | 2 | 45.45455 | 0.008 | 100 | 26 | |
| chrX:154,979,673-155,219,364 | 239691 | q28 | CN Gain | 2 | 0 | 63.63636 | 0 | 97.69119 | 2 |